Term
| The technology to determine the order of base pairs along DNA molecules is called |
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Definition
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| a collection of molecules or cells, all identical to an original molecule or cell |
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Definition
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Definition
Identify genes
Express genes
Mutate genes
Sequence genomes |
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Term
| a collection of chimeric plasmids that include all the genes in a genome |
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Definition
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Term
| deoxyribo endonucleases that (1) recognize specific DNA sequences and (2) hydrolyze a phosphodiester bond on both DNA strands |
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| The 1978 Nobel Prize for Physiology or medicine was awarded to Daniel Nathans, Werner Arber and Hamilton Smith |
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Definition
| Discovered Restriction Enzymes |
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Term
| An enzyme that recognizes a 6-base sequence is called |
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Definition
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Term
| restriction enzymes that cleave DNA chains at selected sites. |
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Term
| Recognition sites in double stranded DNA have a 2-fold axis of symmetry |
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Term
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Definition
Type II and III restriction enzymes cleave DNA chains at selected sites.
Enzymes may recognize 4, 6 or more bases in selecting sites for cleavage. An enzyme that recognizes a 6-base sequence is called a "six-base cutter”.
No ATP requirement.
Recognition sites in double stranded DNA have a 2-fold axis of symmetry – a “palindrome”.
Cleavage can leave staggered or "sticky" ends or can produce "blunt” ends. |
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Term
| joins DNA fragments together |
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Definition
DNA Ligase
Sticky ends that are complementary can be ligated together by DNA ligase I |
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Term
| naturally occurring extrachromosomal, circular, double-stranded DNA molecules |
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Definition
Plasmids
Plasmids can be cleaved by restriction enzymes, leaving sticky or blunt ends.
Artificial plasmids can be constructed by linking new DNA fragments to the sticky ends of plasmid. |
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Term
| a plasmid that can be modified to carry new genes |
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Definition
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Term
| Plasmids useful as cloning vectors must have |
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Definition
An origin of replication.
A selectable marker (antibiotic resistance gene, such as ampr and tetr).
Multiple cloning site (MCS) (site where insertion of foreign DNA will not disrupt replication or inactivate essential markers).
Easy to purify away from host DNA |
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Term
Named for mythological beast with body parts from several creatures.
After cleavage of a plasmid with a restriction enzyme, a foreign DNA fragment can be inserted.
Ends of the plasmid/fragment are closed to form a "recombinant plasmid”.
Plasmid can replicate when placed in a suitable bacterial host. |
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Definition
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Term
| Sequencing a genome can go in one of two directions: |
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Definition
If the genome sequence is unknown and unrelated to another genome, then DNA sequencing techniques that capture kb length reads are useful.
If the genome is known or related to a close evolutionary genome, then sequencing techniques that capture shorter reads can be used. |
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Term
| catalyze the addition of a nucleotide unit using the principle of base complementation |
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Definition
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Term
DNA polymerases catalyze the addition of a nucleotide unit using the principle of base complementation.
NEED: |
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Definition
template: strand to copy
primer: requires a chain that base pairs with the template and has a 3’-OH on which to add
deoxynucleoside triphosphates: dATP, dGTP, dCTP, dTTP |
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Term
| traditional capillary-sequencing technology (dideoxy sequencing): slow but accurate |
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Definition
clone DNA
add primer and DNA polymerase
use a mix of 2’-deoxy and 2’,3’-dideoxy nucleotides
separate nested fragments by gel electrophoresis in a capillary tube
good reads go to 1000 nucleotides |
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Term
| The piece of DNA that holds the foreign DNA is called |
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Definition
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Term
| Useful vectors contain ________ ______________, such as drug resistance genes, so that they can be transformed into host cells |
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Definition
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Term
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Definition
pentose - ribose, 3'-deoxyribose
N-glycosidic bond of 1'-C to N- of nucleic acid base
5'-PO4 group attached via ester bond |
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Definition
A=T, C=G
Principle of complementation |
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Term
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Definition
| Cytosine and Thymine (and Uracil) |
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Definition
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Term
| Reversible strand separation |
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Definition
| can denature with heat (Tm)or OH- (strong alkaline) |
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Term
Using spectrophotometer (nm)
DS or SS absorbs more light |
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Definition
260nm
SS absorbs more light |
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Term
| Agarose gel electrophoresis |
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Definition
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Term
| gel electrophoresis dyes - |
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Definition
intercalating agents (insert in DNA)
ethidium bromide
acridine orange
causes polymerase to think it is a base and causes mutations |
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Term
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Definition
string of amino acids that comprise the:
1) primary sequence of a protein
2) a noncoding RNA that will be used to synthesize or alter genes, transcripts, and proteins
3) the DNA sequences that control the expression of the gene (regulatory DNA sequences) |
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Definition
interrupting sequence
intervening sequence |
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Definition
| DNA sequences that control the expression of the gene |
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Definition
more than one codon/amino acid
read 5' - 3' |
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Definition
methionine (AUG)
tryptophan (UGG) |
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Definition
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Definition
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Definition
uninterrupted string of amino acids
6 reading frames for dsDNA +1 to +3,
-1 to -3
also named Watson and Crick strands or
Coding strand and template strand |
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Term
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Definition
| is the DNA strand that has codons in their DNA form |
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Definition
| is the strand read by RNA polymerase to make complementary RNA strand |
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Definition
mRNA is
hybridized with poly-T primer using oligo dT as a universal primer
make complementary DNA copy with reverse transcriptase
degrade RNA with RNase H
synthesize a second cDNA strand using DNA polymerase; RNA fragment acts as primer
double-stranded cDNA copy of original mRNA |
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Definition
| a DNA polymerase that uses RNA as a template |
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Term
| Average protein molecular weight |
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Definition
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Term
| Average amino acid molecular weight |
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Definition
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Definition
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Term
| 500 amino acid codons requires how many bp? |
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Definition
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Term
| cDNAs derived from mRNA collections with unknown functions are designated |
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Definition
| ESTs - Expressed Sequence Tags |
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Definition
| highly conserved genes/proteins between organisms |
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Term
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Definition
| conserved order of genes in our genome - is often conserved in other genomes |
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Term
Southern blotting
-gel electrophoresis
-nitrocellulose paper |
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Definition
DNA-A technique to create a restriction map of a gene without cloning it
Step 1: digest total genomic DNA with a restriction enzyme to completion
Step 2: Transfer restriction fragments to filter in situ (nitrocellulose paper - cucks buffer with DNa up)
Step 3: Probe filter with labeled cloned ssDNA
Step 4: Detect labeled probe annealed to complementary fragments - visualized by autoradiography
Step 3: |
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Term
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Definition
| same as Southern blotting, but for RNA |
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Term
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Definition
| Expressed in (mature) mRNA |
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Term
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Definition
| measured in terms of nucleotide base pairs per haploid genome |
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Definition
| fish with few introns or repetitive DNA |
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Definition
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Term
| locus control region for human beta-globulin genes |
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Definition
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Definition
multiple copies within one organism
two genes in the same organism encoding a homologous protein |
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Definition
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Term
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Definition
parasitic DNA elements that reproduce via an RNA intermediate
move around genome (transpose)
require reverse transcriptase
comprise approximately 50% of our genome |
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Term
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Definition
long interspersed nuclear elements
up to 6kb in length
20% of DNA
active elements encode reverse transcriptase
many inactive copies
have signature 3'-end reflective of RNA intermediate (Poly-A tail)
most common called L1 |
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Term
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Definition
short interspersed nuclear elements
approximately 300 bp long
transpose through an RNA intermediate
too short to code for reverse transcriptase; rely on L1 reverse transcriptase |
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Definition
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Term
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Definition
called disproportional dwarfism
second copy of the Fgf4 (fibroblast growth factor)gene
recessive gene. Two copies make it dominant
2nd copy has no introns and has a Poly-A tail |
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Term
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Definition
often posses multiple copies of genes with slightly different sequences
arise by duplication of DNA during evolution |
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Term
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Definition
the complex of DNA and protein
approximately half of the protein are histones
the other half are non-histone proteins |
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Term
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Definition
11nm histone octamer
Wrapped 1 3/4 times around core
DNA goes clockwise (left handed helix) around core
In addition to the salt bridges between the basic amino acid side groups and the DNA phosphates, there are 142 H-bonds between the DNA and the core histones of the octamer.
half are between the amino acid backbone of the histones and the sugar-phosphate backbone of DNA.
a few of these H-bonds are to minor groove atoms
Finally, there are hydrophobic interactions between histone proteins and the DNA, as well |
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Term
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Definition
| DNA double helix (2nm) - Nucleosome (11nm) - packed nucleosome (30nm) - extended chromatin (30 & 300nm loops) - condensed chromatin (700nm) - condensed chromosome (1400nm) |
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Term
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Definition
H2a, H2b, H3, H4
approximately 100 amino acids
basic pH (1/5 lysine and arginine)
very conserved (ortholog)
8 histones and 146 bp |
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Term
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Definition
consists of three alpha-helical motifs common to all 4 histones
helps associations needed for octamer |
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Term
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Definition
N-terminal tails
post-translationally modified
provide signal for DNA condensation and gene expression
The N-terminal tails protrude out of the core. They too can interact through electrostatic interaction with the DNA. Their interaction is controlled by protein modification. In addition, tails from different cores can interact to promote additional condensation |
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Term
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Definition
During assembly, the DNA is wrapped around the H3-H4 tetramer.
Two copies of the H2a-H2b dimer are then added. |
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Term
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Definition
histone H1
- H1 binds where DNA enters and exits octamer.
- covers linker DNA
- sets an angle important for further condensation |
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Term
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Definition
Closed for 250 ms
open for 10-50ms
sequence-specific DNA-binding protein can attach when open
It has been shown by kinetic experiments that DNA can unravel from the octamer core for a sufficient amount of time to permit a nonhistone protein to bind. |
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Term
| chromatin remodeling complexes |
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Definition
Cells possess means of changing the position and composition of octamer cores. Some remodeling complexes use ATP energy to slide the octamer cores.
ATP-dependent chromatin remodeling complex
Used to expose promoter region |
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Term
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Definition
The major reasons for exchanging cores are 1) to introduce variant forms of core histones and 2) to remove cores during transcription and replication.
types:
H3.3 - transcriptional activation (maintaining transcriptionally active open state - locked open)
CENP-A - Centromere function and kinetochore assembly (maintaining kinetochore attachment)
H2AX - DNA repair and recombination (attracting DNA repair enzymes)
H2AZ - gene expression, chromosome segregation
macro H2A - transcriptional repression, X-chromosome inactivation |
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Term
zigzag model (two-start helix)
Solenoid model (one-start helix) |
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Definition
| No one quite knows how the 30 nm fiber is organized. One possibility is the zigzag structure. |
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Term
| Higher order condensation requires nonhistone proteins |
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Definition
In the next level of organization the 30 nm fiber forms loops along the axis of the chromosome. A scaffold made of proteins promotes loop formation.
The 60 kb of DNA comprising the β globin gene family forms a loop.
Structural/Scaffolding proteins |
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Term
| DNA that is wrapped clockwise around octamer cores is |
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Definition
| positively supertwisted. Relaxation by topoisomerases makes it negatively supertwisted |
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